However you are a step ahead as I did not read the README.md which suggests that the behavior I was expecting is supposed to be there. However I did a quick test by removing the layouts and pages from mt custom template which completely borked it. Maybe it is supported for layouts only, I will run further tests after learning this.

If the README is correct, the overrides will be picked up from your kunena template layouts directory, but not from the Joomla template (yet). If not present it will revert to the crypsis one.